High througput BLAST-analysis

Question

[noemichael]

Is there a simple and automated way to do a BLAST analysis of 900 genes to find clusters... or should I make a 900x900 table and compare each gene individually with each other?

Thank you for your help!

Answer 1

[Neilfws]

To cluster sequences, I'd consider using CD-HIT rather than BLAST.

Answer 2

[Sishuo Wang]

OrthoMCL is another good choice in addition to CD-HIT as mentioned by Neilfws. Alternatively, you might want to use SiLiX which is very fast and could be used for both nucleotide sequences or amino acid sequences.